Yes, it can work with multiple mats or no mat.

All that matters is that the calibration box that is projected on surface has 90 degree corners and lengths of calibration box are the same as what is entered in the calibration settings in H and W boxes at top of screen.

(also matters that the grid inside the calibration box is accurate all over, but that usually happens automatically, except in some situations of a few projectors having an "auto-keystone" setting that creates an uneven grid inside an accurate calibration box. Turning off auto-keystone fixes that.)

So butt up the mats, and take a tape measure to see what the height and width of the projected calibration box you are creating across the two mats measure. And enter those measurements for your calibration.

Add pics of calibration projected on your mats and I can give you more specific tips.